Microsoft has a wonderful tool which can easily be installed on your server and gives you detailed reports on SEO-bility of your website, specifically:
1. you can run multiple reports to find out if your site has any major SEO issues.
2. not only does the toolkit identifies SEO issues, but also helps you fix them too.
3. it will index all reachable links on your website and provide detailed link-link analysis.
You just need to simply install this toolkit on the webserver where your site is running. You can download the toolkit for free from here.
Also, you can read this useful post from Scott Gu on how to install and use the SEO toolkit on your webserver.
Let me know if you have any additional feedback on this toolkit!